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r-rnadecay 1.30.0
Propagated dependencies: r-tmb@1.9.18 r-scales@1.4.0 r-nloptr@2.2.1 r-gplots@3.2.0 r-ggplot2@4.0.1
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RNAdecay
Licenses: GPL 2
Build system: r
Synopsis: Maximum Likelihood Decay Modeling of RNA Degradation Data
Description:

RNA degradation is monitored through measurement of RNA abundance after inhibiting RNA synthesis. This package has functions and example scripts to facilitate (1) data normalization, (2) data modeling using constant decay rate or time-dependent decay rate models, (3) the evaluation of treatment or genotype effects, and (4) plotting of the data and models. Data Normalization: functions and scripts make easy the normalization to the initial (T0) RNA abundance, as well as a method to correct for artificial inflation of Reads per Million (RPM) abundance in global assessments as the total size of the RNA pool decreases. Modeling: Normalized data is then modeled using maximum likelihood to fit parameters. For making treatment or genotype comparisons (up to four), the modeling step models all possible treatment effects on each gene by repeating the modeling with constraints on the model parameters (i.e., the decay rate of treatments A and B are modeled once with them being equal and again allowing them to both vary independently). Model Selection: The AICc value is calculated for each model, and the model with the lowest AICc is chosen. Modeling results of selected models are then compiled into a single data frame. Graphical Plotting: functions are provided to easily visualize decay data model, or half-life distributions using ggplot2 package functions.

r-rgenometracksdata 0.99.0
Propagated dependencies: r-annotationhub@4.0.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rGenomeTracksData
Licenses: GPL 3+
Build system: r
Synopsis: Demonstration Data from rGenomeTracks Package
Description:

rGenomeTracksData is a collection of data from pyGenomeTracks project. The purpose of this data is testing and demonstration of rGenomeTracks. This package include 14 sample file from different genomic and epigenomic file format.

r-rnamodr-data 1.24.0
Propagated dependencies: r-experimenthubdata@1.36.0 r-experimenthub@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/FelixErnst/RNAmodR.Data
Licenses: Artistic License 2.0
Build system: r
Synopsis: Example data for the RNAmodR package
Description:

RNAmodR.Data contains example data, which is used for vignettes and example workflows in the RNAmodR and dependent packages.

r-roseq 1.22.0
Propagated dependencies: r-pbmcapply@1.5.1 r-limma@3.66.0 r-edger@4.8.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/krishan57gupta/ROSeq
Licenses: GPL 3
Build system: r
Synopsis: Modeling expression ranks for noise-tolerant differential expression analysis of scRNA-Seq data
Description:

ROSeq - A rank based approach to modeling gene expression with filtered and normalized read count matrix. ROSeq takes filtered and normalized read matrix and cell-annotation/condition as input and determines the differentially expressed genes between the contrasting groups of single cells. One of the input parameters is the number of cores to be used.

r-rhesusprobe 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rhesusprobe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type rhesus
Description:

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Rhesus\_probe\_tab.

r-rcwl 1.26.0
Propagated dependencies: r-yaml@2.3.10 r-shiny@1.11.1 r-s4vectors@0.48.0 r-r-utils@2.13.0 r-diagrammer@1.0.11 r-codetools@0.2-20 r-biocparallel@1.44.0 r-batchtools@0.9.18 r-basilisk@1.22.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/Rcwl
Licenses: GPL 2 FSDG-compatible
Build system: r
Synopsis: An R interface to the Common Workflow Language
Description:

The Common Workflow Language (CWL) is an open standard for development of data analysis workflows that is portable and scalable across different tools and working environments. Rcwl provides a simple way to wrap command line tools and build CWL data analysis pipelines programmatically within R. It increases the ease of usage, development, and maintenance of CWL pipelines.

r-rgu34bprobe 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rgu34bprobe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type rgu34b
Description:

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RG-U34B\_probe\_tab.

r-rifi 1.14.0
Propagated dependencies: r-tibble@3.3.0 r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-scales@1.4.0 r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-rlang@1.1.6 r-reshape2@1.4.5 r-nnet@7.3-20 r-nls2@0.3-4 r-ggplot2@4.0.1 r-foreach@1.5.2 r-egg@0.4.5 r-dplyr@1.1.4 r-domc@1.3.8 r-cowplot@1.2.0 r-car@3.1-3
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rifi
Licenses: FSDG-compatible
Build system: r
Synopsis: 'rifi' analyses data from rifampicin time series created by microarray or RNAseq
Description:

rifi analyses data from rifampicin time series created by microarray or RNAseq. rifi is a transcriptome data analysis tool for the holistic identification of transcription and decay associated processes. The decay constants and the delay of the onset of decay is fitted for each probe/bin. Subsequently, probes/bins of equal properties are combined into segments by dynamic programming, independent of a existing genome annotation. This allows to detect transcript segments of different stability or transcriptional events within one annotated gene. In addition to the classic decay constant/half-life analysis, rifi detects processing sites, transcription pausing sites, internal transcription start sites in operons, sites of partial transcription termination in operons, identifies areas of likely transcriptional interference by the collision mechanism and gives an estimate of the transcription velocity. All data are integrated to give an estimate of continous transcriptional units, i.e. operons. Comprehensive output tables and visualizations of the full genome result and the individual fits for all probes/bins are produced.

r-raexexonprobesetlocation 1.15.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RaExExonProbesetLocation
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type RaEx
Description:

This package was automatically created by package AnnotationForge version 1.7.17. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible.

r-rae230a-db 3.13.0
Propagated dependencies: r-org-rn-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rae230a.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix Affymetrix RAE230A Array annotation data (chip rae230a)
Description:

Affymetrix Affymetrix RAE230A Array annotation data (chip rae230a) assembled using data from public repositories.

r-ribor 1.22.0
Propagated dependencies: r-yaml@2.3.10 r-tidyr@1.3.1 r-s4vectors@0.48.0 r-rlang@1.1.6 r-rhdf5@2.54.0 r-hash@2.2.6.3 r-ggplot2@4.0.1 r-dplyr@1.1.4
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/ribor
Licenses: GPL 3
Build system: r
Synopsis: An R Interface for Ribo Files
Description:

The ribor package provides an R Interface for .ribo files. It provides functionality to read the .ribo file, which is of HDF5 format, and performs common analyses on its contents.

r-rgu34c-db 3.13.0
Propagated dependencies: r-org-rn-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rgu34c.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix Affymetrix RG_U34C Array annotation data (chip rgu34c)
Description:

Affymetrix Affymetrix RG_U34C Array annotation data (chip rgu34c) assembled using data from public repositories.

r-rae230b-db 3.13.0
Propagated dependencies: r-org-rn-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rae230b.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix Affymetrix RAE230B Array annotation data (chip rae230b)
Description:

Affymetrix Affymetrix RAE230B Array annotation data (chip rae230b) assembled using data from public repositories.

r-rscudo 1.26.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-s4vectors@0.48.0 r-igraph@2.2.1 r-biocgenerics@0.56.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/Matteo-Ciciani/scudo
Licenses: GPL 3
Build system: r
Synopsis: Signature-based Clustering for Diagnostic Purposes
Description:

SCUDO (Signature-based Clustering for Diagnostic Purposes) is a rank-based method for the analysis of gene expression profiles for diagnostic and classification purposes. It is based on the identification of sample-specific gene signatures composed of the most up- and down-regulated genes for that sample. Starting from gene expression data, functions in this package identify sample-specific gene signatures and use them to build a graph of samples. In this graph samples are joined by edges if they have a similar expression profile, according to a pre-computed similarity matrix. The similarity between the expression profiles of two samples is computed using a method similar to GSEA. The graph of samples can then be used to perform community clustering or to perform supervised classification of samples in a testing set.

r-regionalst 1.8.0
Propagated dependencies: r-toast@1.24.0 r-tibble@3.3.0 r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-shiny@1.11.1 r-seurat@5.3.1 r-scater@1.38.0 r-s4vectors@0.48.0 r-rcolorbrewer@1.1-3 r-magrittr@2.0.4 r-gridextra@2.3 r-ggplot2@4.0.1 r-fgsea@1.36.0 r-dplyr@1.1.4 r-colorspace@2.1-2 r-biocstyle@2.38.0 r-bayesspace@1.20.0 r-assertthat@0.2.1
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RegionalST
Licenses: GPL 3
Build system: r
Synopsis: Investigating regions of interest and performing regional cell type-specific analysis with spatial transcriptomics data
Description:

This package analyze spatial transcriptomics data through cross-regional cell type-specific analysis. It selects regions of interest (ROIs) and identifys cross-regional cell type-specific differential signals. The ROIs can be selected using automatic algorithm or through manual selection. It facilitates manual selection of ROIs using a shiny application.

r-rcollectl 1.10.0
Dependencies: collectl@4.3.1
Propagated dependencies: r-processx@3.8.6 r-lubridate@1.9.4 r-ggplot2@4.0.1
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/vjcitn/Rcollectl
Licenses: Artistic License 2.0
Build system: r
Synopsis: Help use collectl with R in Linux, to measure resource consumption in R processes
Description:

Provide functions to obtain instrumentation data on processes in a unix environment. Parse output of a collectl run. Vizualize aspects of system usage over time, with annotation.

r-rcaspar 1.56.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RCASPAR
Licenses: GPL 3+
Build system: r
Synopsis: package for survival time prediction based on a piecewise baseline hazard Cox regression model.
Description:

The package is the R-version of the C-based software \boldCASPAR (Kaderali,2006: \urlhttp://bioinformatics.oxfordjournals.org/content/22/12/1495). It is meant to help predict survival times in the presence of high-dimensional explanatory covariates. The model is a piecewise baseline hazard Cox regression model with an Lq-norm based prior that selects for the most important regression coefficients, and in turn the most relevant covariates for survival analysis. It was primarily tried on gene expression and aCGH data, but can be used on any other type of high-dimensional data and in disciplines other than biology and medicine.

r-rcellminerdata 2.32.0
Propagated dependencies: r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rcellminerData
Licenses: FSDG-compatible
Build system: r
Synopsis: rcellminerData: Molecular Profiles and Drug Response for the NCI-60 Cell Lines
Description:

The NCI-60 cancer cell line panel has been used over the course of several decades as an anti-cancer drug screen. This panel was developed as part of the Developmental Therapeutics Program (DTP, http://dtp.nci.nih.gov/) of the U.S. National Cancer Institute (NCI). Thousands of compounds have been tested on the NCI-60, which have been extensively characterized by many platforms for gene and protein expression, copy number, mutation, and others (Reinhold, et al., 2012). The purpose of the CellMiner project (http://discover.nci.nih.gov/ cellminer) has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data.

r-ricecdf 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/ricecdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: ricecdf
Description:

This package provides a package containing an environment representing the Rice.cdf file.

r-rat2302probe 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rat2302probe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type rat2302
Description:

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Rat230\_2\_probe\_tab.

r-rnbeads-rn5 1.42.0
Propagated dependencies: r-genomicranges@1.62.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RnBeads.rn5
Licenses: GPL 3
Build system: r
Synopsis: RnBeads.rn5
Description:

Automatically generated RnBeads annotation package for the assembly rn5.

r-rhdf5client 1.32.0
Propagated dependencies: r-rjson@0.2.23 r-httr@1.4.7 r-delayedarray@0.36.0 r-data-table@1.17.8
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rhdf5client
Licenses: Artistic License 2.0
Build system: r
Synopsis: Access HDF5 content from HDF Scalable Data Service
Description:

This package provides functionality for reading data from HDF Scalable Data Service from within R. The HSDSArray function bridges from HSDS to the user via the DelayedArray interface. Bioconductor manages an open HSDS instance graciously provided by John Readey of the HDF Group.

r-runibic 1.32.0
Propagated dependencies: r-testthat@3.3.0 r-summarizedexperiment@1.40.0 r-rcpp@1.1.0 r-biclust@2.0.3.1
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: http://github.com/athril/runibic
Licenses: Expat
Build system: r
Synopsis: runibic: row-based biclustering algorithm for analysis of gene expression data in R
Description:

This package implements UbiBic algorithm in R. This biclustering algorithm for analysis of gene expression data was introduced by Zhenjia Wang et al. in 2016. It is currently considered the most promising biclustering method for identification of meaningful structures in complex and noisy data.

r-rqt 1.36.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-runit@0.4.33.1 r-ropls@1.42.0 r-pls@2.8-5 r-metap@1.12 r-matrix@1.7-4 r-glmnet@4.1-10 r-compquadform@1.4.4 r-car@3.1-3
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/izhbannikov/rqt
Licenses: GPL 2+ GPL 3+
Build system: r
Synopsis: rqt: utilities for gene-level meta-analysis
Description:

Despite the recent advances of modern GWAS methods, it still remains an important problem of addressing calculation an effect size and corresponding p-value for the whole gene rather than for single variant. The R- package rqt offers gene-level GWAS meta-analysis. For more information, see: "Gene-set association tests for next-generation sequencing data" by Lee et al (2016), Bioinformatics, 32(17), i611-i619, <doi:10.1093/bioinformatics/btw429>.

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Total results: 68655